No, it doesn't depend on the Addon Manager itself. There are no explicit checks made on FS9.EXE, and it doesn't even change if one has the official FS9.EXE or a modified FS9.EXE to bypass the CD check at start. In both cases, Addon Manager will work.
Instead, the fact that you changed the memory allocation for the FS9 executable (I presume you added the /LARGEADDRESSAWARE flag), might lead to believe that this has an unexpected effect on the internal allocation of FS modules, confusing bglman.dll, that expects some things to be at a specific address in ram. There are some safety measures, because (for example) the different ram allocation of different mainboards based on agp, pci or pci-express, is already taken care of. But apparently, the /LARGEADDRESSAWARE flag does something else.
Well, my compliements to you because that "common workaround" is not really *that* common, since you are the first to report this problem since 2005 when we started usign Addon Manager...
I might have a look into it, but I can't promise anything.